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Periasamy R, Crdenas P, Kurian PJ, Ingole B, Samaai T. Is the North Atlantic Geodia barretti (Porifera, Tetractinellida, Geodiidae) present on the Southwest Indian Ridge? Zootaxa 2023; 5380:461-474. [PMID: 38221298 DOI: 10.11646/zootaxa.5380.5.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Indexed: 01/16/2024]
Abstract
There are currently 163 species of Geodia Lamarck, 1815 described worldwide, many of which are found in deep waters, but none of which have been recorded from the Southwest Indian Ridge (SWIR). Spicule morphology and barcodes (Folmer COI, 28S (C2D2), partial 18S) suggest that a specimen of Geodia collected on the SWIR at a depth of 2236 m is closely comparable to Geodia barretti Bowerbank, 1858. Geodia barretti is the most studied and thus well-known deep-sea Geodia species, due to its wide North Atlantic distribution and key role in boreal sponge grounds. This unexpected and markedly disjunct record would extend the distribution range of this species considerably, consequently challenging our knowledge about interoceanic deep-sea sponges.
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Affiliation(s)
- Rengaiyan Periasamy
- National Centre for Polar and Ocean Research; Headland Sada; Ministry of Earth Sciences; Vasco-da-Gama; Goa; India.
| | - Paco Crdenas
- Pharmacognosy; Department of Pharmaceutical Biosciences; Uppsala University; Uppsala; Sweden; Museum of Evolution; Uppsala University; Norbyvgen 16; 752 36 Uppsala; Sweden.
| | - Palayil John Kurian
- National Centre for Polar and Ocean Research; Headland Sada; Ministry of Earth Sciences; Vasco-da-Gama; Goa; India.
| | - Baban Ingole
- National Centre for Polar and Ocean Research; Headland Sada; Ministry of Earth Sciences; Vasco-da-Gama; Goa; India.
| | - Toufiek Samaai
- Department of Forestry; Fisheries; and Environment: Oceans and Coasts Research; Cape Town; South Africa; University of the Western Cape; Biodiversity Conservation Department; Bellville; Cape Town; South Africa; University of Cape Town; Biological Sciences; Rondebosch; Cape Town; South Africa.
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2
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Selifanova M, Demianchenko O, Noskova E, Pitikov E, Skvortsov D, Drozd J, Vatolkina N, Apel P, Kolodyazhnaya E, Ezhova MA, Tzetlin AB, Neretina TV, Knorre DA. ORFans in Mitochondrial Genomes of Marine Polychaete Polydora. Genome Biol Evol 2023; 15:evad219. [PMID: 38019573 PMCID: PMC10721130 DOI: 10.1093/gbe/evad219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFan" regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.
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Affiliation(s)
- Maria Selifanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Demianchenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta Noskova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Egor Pitikov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Denis Skvortsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Jana Drozd
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Nika Vatolkina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Polina Apel
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Kolodyazhnaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Margarita A Ezhova
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander B Tzetlin
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Neretina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Science, Moscow, Russia
| | - Dmitry A Knorre
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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3
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Feng H, Lv S, Li R, Shi J, Wang J, Cao P. Mitochondrial genome comparison reveals the evolution of cnidarians. Ecol Evol 2023; 13:e10157. [PMID: 37325715 PMCID: PMC10261974 DOI: 10.1002/ece3.10157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Cnidarians are the most primitive metazoans, but their evolutionary relationships are poorly understood, although recent studies present several phylogenetic hypotheses. Here, we collected 266 complete cnidarian mitochondrial genomes and re-evaluated the phylogenetic relationships between the major lineages. We described the gene rearrangement patterns of Cnidaria. Anthozoans had significantly greater mitochondrial genome size and lower A + T content than medusozoans. Most of the protein-coding genes in anthozoans such as COX 13, ATP6, and CYTB displayed a faster rate of evolution based on selection analysis. There were 19 distinct patterns of mitochondrial gene order, including 16 unique gene orders in anthozoans and 3 mtDNA gene orders pattern in medusozoans, were identified among cnidarians. The gene order arrangement suggested that a linearized mtDNA structure may be more conducive to Medusozoan mtDNA stability. Based on phylogenetic analyses, the monophyly of the Anthozoa was strongly supported compared to previous mitochondrial genome-based analyses rather than octocorals forming a sister group relationship with medusozoans. In addition, Staurozoa were more closely related to Anthozoa than to Medusozoa. In conclusion, these results largely support the traditional phylogenetic view of the relationships of cnidarians and provide new insights into the evolutionary processes for studying the most ancient animal radiations.
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Affiliation(s)
- Hui Feng
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Sitong Lv
- Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Rong Li
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Jing Shi
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Jianxing Wang
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
| | - Pinglin Cao
- Marine Microorganism Ecological & Application LabZhejiang Ocean UniversityZhoushanChina
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Shimpi GG, Bentlage B. Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes. Bioessays 2023; 45:e2200190. [PMID: 36412071 DOI: 10.1002/bies.202200190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.
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Quek ZBR, Ng JY, Jain SS, Long JXS, Lim SC, Tun K, Huang D. Low genetic diversity and predation threaten a rediscovered marine sponge. Sci Rep 2022; 12:22499. [PMID: 36577798 PMCID: PMC9797562 DOI: 10.1038/s41598-022-26970-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Discovered in 1819 in the tropical waters off Singapore, the magnificent Neptune's cup sponge Cliona patera (Hardwicke, 1820) was harvested for museums and collectors until it was presumed extinct worldwide for over a century since 1907. Recently in 2011, seven living individuals were rediscovered in Singapore with six relocated to a marine protected area in an effort to better monitor and protect the population, as well as to enhance external fertilisation success. To determine genetic diversity within the population, we sequenced the complete mitochondrial genomes and nuclear ribosomal DNA of these six individuals and found extremely limited variability in their genes. The low genetic diversity of this rediscovered population is confirmed by comparisons with close relatives of C. patera and could compromise the population's ability to recover from environmental and anthropogenic pressures associated with the highly urbanised coastlines of Singapore. This lack of resilience is compounded by severe predation which has been shrinking sponge sizes by up to 5.6% every month. Recovery of this highly endangered population may require ex situ approaches and crossbreeding with other populations, which are also rare.
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Affiliation(s)
- Z. B. Randolph Quek
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Juat Ying Ng
- grid.4280.e0000 0001 2180 6431School of Design and Environment, National University of Singapore, Singapore, Singapore ,grid.467827.80000 0004 0620 8814National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Sudhanshi S. Jain
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - J. X. Sean Long
- grid.462738.c0000 0000 9091 4551Republic Polytechnic, Singapore, Singapore
| | - Swee Cheng Lim
- grid.4280.e0000 0001 2180 6431Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Karenne Tun
- grid.467827.80000 0004 0620 8814National Biodiversity Centre, National Parks Board, Singapore, Singapore
| | - Danwei Huang
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Centre for Nature-Based Climate Solutions, National University of Singapore, Singapore, Singapore
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The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa. Genes (Basel) 2021; 12:genes12122030. [PMID: 34946978 PMCID: PMC8700879 DOI: 10.3390/genes12122030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.
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Rider HJ, MacFarland AK, Rape CJ, Engster SP, Bogantes VE, Janosik AM. Characterization of the complete mitochondrial genome of Spheciospongia vesparium (Demospongiae, Clionaida, Clionaidae). Mitochondrial DNA B Resour 2021; 7:28-29. [PMID: 34912961 PMCID: PMC8667908 DOI: 10.1080/23802359.2021.2006815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Loggerhead sponge (Spheciospongia vesparium) is an ecologically important marine species of sponge that provides habitat and food sources to biodiversity hotspots in the Caribbean Sea and along the coasts of Florida. In this study, the complete mitochondrial genome of the sponge, S. vesparium was sequenced and reported. The mitochondrial genome of S. vesparium was 21,763 base pairs, and consisted of 14 protein-coding genes, 26 tRNA genes, and two rRNA genes. The total nucleotide content comprised 31.01% A, 36.04% T, 11.08% C, and 21.88% G, with a lower GC content of 32.95%. This study provides a phylogenetic analysis of S. vesparium and relative sponges in Demospongiae.
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Affiliation(s)
- Hunter J Rider
- Department of Biology, University of West Florida, Pensacola, FL, USA
| | | | | | | | | | - Alexis M Janosik
- Department of Biology, University of West Florida, Pensacola, FL, USA
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Sureshan SC, Tanavade RV, Ghosh S, Ghosh S, Sella RN, Mohideen HS. Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India. Sci Rep 2021; 11:23738. [PMID: 34887433 PMCID: PMC8660866 DOI: 10.1038/s41598-021-02881-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/18/2021] [Indexed: 11/09/2022] Open
Abstract
Oxycarenus laetus is a seed-sap sucking pest affecting a variety of crops, including cotton plants. Rising incidence and pesticide resistance by O. laetus have been reported from India and neighbouring countries. In this study, O. laetus samples were collected from Bhatinda and Coimbatore (India). Pure mtDNA was isolated and sequenced using Illumina MiSeq. Both the samples were found to be identical species (99.9%), and the complete genome was circular (15,672 bp), consisting of 13 PCGs, 2 rRNA, 23 tRNA genes, and a 962 bp control region. The mitogenome is 74.1% AT-rich, 0.11 AT, and - 0.19 GC skewed. All the genes had ATN as the start codon except cox1 (TTG), and an additional trnT was predicted. Nearly all tRNAs folded into the clover-leaf structure, except trnS1 and trnV. The intergenic space between trnH and nad4, considered as a synapomorphy of Lygaeoidea, was displaced. Two 5 bp motifs AATGA and ACCTA, two tandem repeats, and a few microsatellite sequences, were also found. The phylogenetic tree was constructed using 36 mitogenomes from 7 super-families of Hemiptera by employing rigorous bootstrapping and ML. Ours is the first study to sequence the complete mitogenome of O. laetus or any Oxycarenus species. The findings from this study would further help in the evolutionary studies of Lygaeidae.
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Affiliation(s)
- Shruthi Chalil Sureshan
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Ruchi Vivekanand Tanavade
- grid.412742.60000 0004 0635 5080Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Sewali Ghosh
- Department of Advanced Zoology and Biotechnology, Guru Nanak College, Chennai, 600042 Tamil Nadu India
| | - Saswati Ghosh
- grid.506009.aDepartment of Virology, King Institute of Preventive Medicine and Research, Chennai, 600032 Tamil Nadu India
| | - Raja Natesan Sella
- grid.412742.60000 0004 0635 5080Membrane Protein Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203 Tamil Nadu India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Tamil Nadu, India.
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Abstract
The evolutionary theory of aging has set the foundations for a comprehensive understanding of aging. The biology of aging has listed and described the "hallmarks of aging," i.e., cellular and molecular mechanisms involved in human aging. The present paper is the first to infer the order of appearance of the hallmarks of bilaterian and thereby human aging throughout evolution from their presence in progressively narrower clades. Its first result is that all organisms, even non-senescent, have to deal with at least one mechanism of aging - the progressive accumulation of misfolded or unstable proteins. Due to their cumulation, these mechanisms are called "layers of aging." A difference should be made between the first four layers of unicellular aging, present in some unicellular organisms and in all multicellular opisthokonts, that stem and strike "from the inside" of individual cells and span from increasingly abnormal protein folding to deregulated nutrient sensing, and the last four layers of metacellular aging, progressively appearing in metazoans, that strike the cells of a multicellular organism "from the outside," i.e., because of other cells, and span from transcriptional alterations to the disruption of intercellular communication. The evolution of metazoans and eumetazoans probably solved the problem of aging along with the problem of unicellular aging. However, metacellular aging originates in the mechanisms by which the effects of unicellular aging are kept under control - e.g., the exhaustion of stem cells that contribute to replace damaged somatic cells. In bilaterians, additional functions have taken a toll on generally useless potentially limited lifespan to increase the fitness of organisms at the price of a progressively less efficient containment of the damage of unicellular aging. In the end, this picture suggests that geroscience should be more efficient in targeting conditions of metacellular aging rather than unicellular aging itself.
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Affiliation(s)
- Maël Lemoine
- CNRS, ImmunoConcEpT, UMR 5164, Univ. Bordeaux, Bordeaux, France
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The complete mitochondrial genome of a parasite at the animal-fungal boundary. Parasit Vectors 2020; 13:81. [PMID: 32066491 PMCID: PMC7027106 DOI: 10.1186/s13071-020-3926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 02/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sphaerothecum destruens is an obligate intracellular fish parasite which has been identified as a serious threat to freshwater fishes. Taxonomically, S. destruens belongs to the order Dermocystida within the class Ichthyosporea (formerly referred to as Mesomycetozoea), which sits at the animal-fungal boundary. Mitochondrial DNA (mtDNA) sequences can be valuable genetic markers for species detection and are increasingly used in environmental DNA (eDNA) based species detection. Furthermore, mtDNA sequences can be used in epidemiological studies by informing detection, strain identification and geographical spread. METHODS We amplified the entire mitochondrial (mt) genome of S. destruens in two overlapping long fragments using primers designed based on the cox1, cob and nad5 partial sequences. The mt-genome architecture of S. destruens was then compared to close relatives to gain insights into its evolution. RESULTS The complete mt-genome of Sphaerothecum destruens is 23,939 bp in length and consists of 47 genes including 21 protein-coding genes, 2 rRNA, 22 tRNA and two unidentified open reading frames. The mitochondrial genome of S. destruens is intronless and compact with a few intergenic regions and includes genes that are often missing from animal and fungal mt-genomes, such as, the four ribosomal proteins (small subunit rps13 and 14; large subunit rpl2 and 16), tatC (twin-arginine translocase component C), and ccmC and ccmF (cytochrome c maturation protein ccmC and heme lyase). CONCLUSIONS We present the first mt-genome of S. destruens which also represents the first mt-genome for the order Dermocystida. The availability of the mt-genome can assist the detection of S. destruens and closely related parasites in eukaryotic diversity surveys using eDNA and assist epidemiological studies by improving molecular detection and tracking the parasite's spread. Furthermore, as the only representative of the order Dermocystida, its mt-genome can be used in the study of mitochondrial evolution of the unicellular relatives of animals.
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Schultz DT, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SH. Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii. PeerJ 2020; 8:e8356. [PMID: 32025367 PMCID: PMC6991124 DOI: 10.7717/peerj.8356] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/04/2019] [Indexed: 11/20/2022] Open
Abstract
To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.
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Affiliation(s)
- Darrin T. Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Jordan M. Eizenga
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Warren R. Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Steven H.D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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12
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Bautista-Guerrero E, Llera-Herrera R, Carballo JL, Rocha-Olivares A, Rodríguez-Troncoso AP, González-Castillo A, Cruz-Barraza JA. The complete mitogenome of excavating sponge Thoosa mismalolli (Demospongiae, Tetractinellida, Thoosidae) from Northeastern Tropical Pacific. Mitochondrial DNA B Resour 2020; 5:689-691. [PMID: 33366705 PMCID: PMC7748439 DOI: 10.1080/23802359.2020.1714499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The complete mitogenome of Thoosa mismalolli Carballo, Cruz-Barraza & Gómez, 2004 (Tetractinellida, Thoosidae) was sequenced. This is the first complete mitogenome of the suborden Thoosina and the third Tetractinellid so far. The mitochondrial genome of T. mismalolli was assembled based on reads obtained with the Illumina HiSeq platform. The length of complete mitogenome is 19,019 bp long and contained 14 protein-coding genes and 23 tRNA, with two tRNA genes. Phylogenetic reconstruction (maximum-likelihood) based on mitogenome of Tetractinellids, supports T. mismalolli as a sister group. This result is congruent with those obtained with molecular markers (CO1, 18S, and 28S), supporting the monophyletic status of Thoosa and providing additional molecular data in favor of the suborder Thoosina.
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Affiliation(s)
- Eric Bautista-Guerrero
- Laboratorio de Ecología Marina, Centro de Investigaciones Costeras, Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Mexico
| | - Raúl Llera-Herrera
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, Mexico
| | - José L. Carballo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, Mexico
| | | | - Alma P. Rodríguez-Troncoso
- Laboratorio de Ecología Marina, Centro de Investigaciones Costeras, Centro Universitario de la Costa, Universidad de Guadalajara, Puerto Vallarta, Mexico
| | - Adrian González-Castillo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, Mexico
| | - José A. Cruz-Barraza
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), Mazatlán, Mexico
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Morrow C, Cárdenas P, Boury-Esnault N, Picton B, McCormack G, Van Soest R, Collins A, Redmond N, Maggs C, Sigwart J, Allcock LA. Integrating morphological and molecular taxonomy with the revised concept of Stelligeridae (Porifera: Demospongiae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six new species of Paratimea, the resurrection of Halicnemia gallica and a better understanding of the characters uniting Stelligeridae. A new species of Heteroxya is also described. We demonstrate that many of the taxa assigned to Heteroxyidae are more closely related to other families, and we propose several changes to the classification of Heteroscleromorpha. Desmoxyidae is resurrected from synonymy and transferred to Poecilosclerida; Higginsia anfractuosa is transferred to Hymedesmiidae, and a new genus, Hooperia, is erected for its reception; Higginsia durissima is returned to Bubaris (Bubaridae); Higginsia fragilis is transferred to Spanioplon (Hymedesmiidae); Hemiasterella camelus is transferred to Paratimea; and Raspailia (Parasyringella) australiensis and Ceratopsion axiferum are transferred to Adreus (Hemiasterellidae).
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Affiliation(s)
- Christine Morrow
- School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
- Queen’s University Marine Laboratory, Portaferry, Northern Ireland, UK
- National Museums Northern Ireland, Holywood, Northern Ireland, UK
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC, Uppsala, Sweden
| | - Nicole Boury-Esnault
- IMBE, CNRS, Aix-Marseille University, University Avignon, IRD, Station marine d’Endoume, Marseille, France
| | - Bernard Picton
- National Museums Northern Ireland, Holywood, Northern Ireland, UK
| | - Grace McCormack
- School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Rob Van Soest
- Netherlands Centre for Biodiversity Naturalis, Leiden, The Netherlands
| | - Allen Collins
- National Systematics Laboratory, National Museum of Natural History, MRC-153, Smithsonian Institution, Washington, DC, USA
| | - Niamh Redmond
- Smithsonian Institution DNA Barcode Network, National Museum of Natural History, MRC-183, Smithsonian Institution, Washington, DC, USA
| | - Christine Maggs
- Joint Nature Conservation Committee, Monkstone House, Peterborough, UK
| | - Julia Sigwart
- Queen’s University Marine Laboratory, Portaferry, Northern Ireland, UK
| | - Louise A Allcock
- School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, Ireland
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14
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Schuster A, Vargas S, Knapp IS, Pomponi SA, Toonen RJ, Erpenbeck D, Wörheide G. Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model. BMC Evol Biol 2018; 18:114. [PMID: 30021516 PMCID: PMC6052604 DOI: 10.1186/s12862-018-1230-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Approximately 80% of all described extant sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions on the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be "calibrated" with additional data such as fossils. Here, we calibrate the molecular data with the fossilized birth-death model, which compared to strict node dating, allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (~500 Ma), to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To infer a dated phylogeny of Demospongiae we assembled the mitochondrial genomes of six desma-bearing demosponges from reduced-representation genomic libraries. The total dataset included 33 complete demosponge mitochondrial genomes and 30 fossils. RESULTS Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed recent (~18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae (~315 Ma), the Astrophorina (~240 Ma), the Spirophorina (~120 Ma) and the family Corallistidae (~188 Ma) all of which are considered as key groups for dating the Demospongiae due to their extraordinary rich and continuous fossil history. CONCLUSION This study provides novel insights into the evolution of Demospongiae. Observed discrepancies of our dated phylogeny with their putative first fossil appearance dates are discussed for selected sponge groups. For instance, a Carboniferous origin of the order Tetractinellida seems to be too late, compared to their first appearance in the fossil record in the Middle Cambrian. This would imply that Paleozoic spicule forms are not homologous to post-Paleozoic forms.
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Affiliation(s)
- Astrid Schuster
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Ingrid S. Knapp
- Hawai‘i Institute of Marine Biology, 46-007 Lilipuna Road, Kāne‘ohe, Hawai‘i 96744 USA
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute-Florida Atlantic University, 5600 U.S. 1 North, Ft Pierce, FL 34946 USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, 46-007 Lilipuna Road, Kāne‘ohe, Hawai‘i 96744 USA
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
- SNSB - Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, 80333 Munich, Germany
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15
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Schuster A, Lopez JV, Becking LE, Kelly M, Pomponi SA, Wörheide G, Erpenbeck D, Cárdenas P. Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding. BMC Evol Biol 2017; 17:82. [PMID: 28320321 PMCID: PMC5360047 DOI: 10.1186/s12862-017-0928-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns. RESULTS For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated. CONCLUSION This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.
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Affiliation(s)
- Astrid Schuster
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004 USA
| | - Leontine E. Becking
- Marine Animal Ecology, Wageningen University & Research Centre, P.O. Box 3700, AH, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Marine Zoology Department, PO Box 9517, 2300 RA, Leiden, The Netherlands
| | - Michelle Kelly
- National Centre for Aquatic Biodiversity and Biosecurity, National Institute of Water and Atmospheric Research, P.O. Box 109–695, Newmarket, Auckland, New Zealand
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute-Florida Atlantic University, 5600 U.S. 1 North, Ft Pierce, FL 34946 USA
| | - Gert Wörheide
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
- SNSB - Bavarian State Collections of Palaeontology and Geology, Richard-Wagner Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth- & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner Str. 10, 80333 Munich, Germany
| | - Paco Cárdenas
- Department of Medicinal Chemistry, Division of Pharmacognosy, BioMedical Center, Uppsala University, Husargatan 3, 75123 Uppsala, Sweden
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16
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Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals. PLoS One 2016; 11:e0165072. [PMID: 27755612 PMCID: PMC5068742 DOI: 10.1371/journal.pone.0165072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia.
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17
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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18
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Zhang Y, Huang D, Wang D, Ding S. The complete mitochondrial genome of sponge Tethya sp. (Demospongiae, Tethyida, Tethyidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:472-474. [PMID: 33473525 PMCID: PMC7799499 DOI: 10.1080/23802359.2016.1186518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The complete mitochondrial genome of Tethya sp. was studied. This is the second complete mitochondrial report on the family Tethyidae. The mitochondrial genome of Tethya sp. is 20,582 bp in length, containing 14 protein-coding genes and 25 tRNA genes, with 2 rRNA genes. Our phylogenetic result suggested that Tethya sp. converged well with Tethya actinia, which further verified the morphological result. We anticipate our study to shed light on future molecular studies of demosponges.
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Affiliation(s)
- Yuan Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China.,Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Dan Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China.,Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Dexiang Wang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China.,Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Shaoxiong Ding
- Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
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19
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Halanych KM. The ctenophore lineage is older than sponges? That cannot be right! Or can it? ACTA ACUST UNITED AC 2015; 218:592-7. [PMID: 25696822 DOI: 10.1242/jeb.111872] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent phylogenetic analyses resulting from collection of whole genome data suggest that ctenophores, or comb jellies, are sister to all other animals. Even before publication, this result prompted discussion among researchers. Here, I counter common criticisms raised about this result and show that assumptions placing sponges as the basal-most extant animal lineage are based on limited evidence and questionable premises. For example, the idea that sponges are simple and the reported similarity of sponge choanocytes to Choanflagellata do not provide useful characters for determining the positions of sponges within the animal tree. Intertwined with discussion of basal metazoan phylogeny is consideration of the evolution of neuronal systems. Recent data show that neural systems of ctenophores are vastly different from those of other animals and use different sets of cellular and genetic mechanisms. Thus, neural systems appear to have at least two independent origins regardless of whether ctenophores or sponges are the earliest branching extant animal lineage.
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Affiliation(s)
- Kenneth M Halanych
- Department of Biological Sciences, 101 Life Sciences Building, Auburn University, Auburn, AL 36849, USA Friday Harbor Laboratories, 620 University Road, University of Washington, Friday Harbor, WA 98250, USA
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20
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Igloi GL, Leisinger AK. Identity elements for the aminoacylation of metazoan mitochondrial tRNA(Arg) have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment. RNA Biol 2015; 11:1313-23. [PMID: 25603118 PMCID: PMC4615739 DOI: 10.1080/15476286.2014.996094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA(Ser)UCU. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.
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Affiliation(s)
- Gabor L Igloi
- a Institute of Biology III ; University of Freiburg ; Freiburg , Germany
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21
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Knapp IS, Forsman ZH, Williams GJ, Toonen RJ, Bell JJ. Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific. PeerJ 2015; 3:e1170. [PMID: 26339548 PMCID: PMC4558080 DOI: 10.7717/peerj.1170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/20/2015] [Indexed: 11/30/2022] Open
Abstract
Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawai'i using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawai'i and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawai'i remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.
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Affiliation(s)
- Ingrid S. Knapp
- School of Ocean and Earth Science and Technology, Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Manoa, Kāneʻohe, HI, USA
| | - Zac H. Forsman
- School of Ocean and Earth Science and Technology, Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Manoa, Kāneʻohe, HI, USA
| | - Gareth J. Williams
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, CA, USA
| | - Robert J. Toonen
- School of Ocean and Earth Science and Technology, Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Manoa, Kāneʻohe, HI, USA
| | - James J. Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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22
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Sahyoun AH, Hölzer M, Jühling F, Höner zu Siederdissen C, Al-Arab M, Tout K, Marz M, Middendorf M, Stadler PF, Bernt M. Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes. Nucleic Acids Res 2015; 43:8044-56. [PMID: 26227972 PMCID: PMC4783518 DOI: 10.1093/nar/gkv746] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/11/2015] [Indexed: 12/03/2022] Open
Abstract
Remolding of tRNAs is a well-documented process in mitochondrial genomes that changes the identity of a tRNA. It involves a duplication of a tRNA gene, a mutation that changes the anticodon and the loss of the ancestral tRNA gene. The net effect is a functional tRNA that is more closely related to tRNAs of a different alloacceptor family than to tRNAs with the same anticodon in related species. Beyond being of interest for understanding mitochondrial tRNA function and evolution, tRNA remolding events can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. Therefore, it is important to identify and catalog these events. Here we describe novel methods to detect tRNA remolding in large-scale data sets and apply them to survey tRNA remolding throughout animal evolution. We identify several novel remolding events in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived from ancestral events.
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Affiliation(s)
- Abdullah H Sahyoun
- Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany Bioinformatics Unit and Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Frank Jühling
- Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Christian Höner zu Siederdissen
- Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
| | - Marwa Al-Arab
- Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon
| | - Kifah Tout
- Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Martin Middendorf
- Parallel Computing and Complex Systems Group, Department of Computer Science, Leipzig University, Augustusplatz 10, D-04109 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany Fraunhofer Institut für Zelltherapie und Immunologie Perlickstraße 1, D-04103 Leipzig, Germany Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, Leipzig University, Augustusplatz 10, D-04109 Leipzig, Germany
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Foox J, Brugler M, Siddall ME, Rodríguez E. Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2826-32. [PMID: 26104159 DOI: 10.3109/19401736.2015.1053114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Six complete and three partial actiniarian mitochondrial genomes were amplified in two semi-circles using long-range PCR and pyrosequenced in a single run on a 454 GS Junior, doubling the number of complete mitogenomes available within the order. Typical metazoan mtDNA features included circularity, 13 protein-coding genes, 2 ribosomal RNA genes, and length ranging from 17,498 to 19,727 bp. Several typical anthozoan mitochondrial genome features were also observed including the presence of only two transfer RNA genes, elevated A + T richness ranging from 54.9 to 62.4%, large intergenic regions, and group 1 introns interrupting NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit I, the latter of which possesses a homing endonuclease gene. Within the sea anemone Alicia sansibarensis, we report the first mitochondrial gene order rearrangement within the Actiniaria, as well as putative novel non-canonical protein-coding genes. Phylogenetic analyses of all 13 protein-coding and 2 ribosomal genes largely corroborated current hypotheses of sea anemone interrelatedness, with a few lower-level differences.
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Affiliation(s)
- Jonathan Foox
- a Richard Gilder Graduate School, American Museum of Natural History , New York , NY , USA
| | - Mercer Brugler
- b Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History , New York , NY , USA , and.,c Biological Sciences Department, NYC College of Technology (CUNY) , Brooklyn , NY , USA
| | - Mark Edward Siddall
- a Richard Gilder Graduate School, American Museum of Natural History , New York , NY , USA .,b Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History , New York , NY , USA , and
| | - Estefanía Rodríguez
- a Richard Gilder Graduate School, American Museum of Natural History , New York , NY , USA .,b Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History , New York , NY , USA , and
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Abstract
We discovered for the first time a mitochondrial intron in a non-tetillid demosponge, which sheds new light on the interpretation of mitochondrial intron evolution among non-bilaterian animals and has consequences for phylogenetic and DNA barcoding studies. The newly discovered class 1 intron of Aplysinella rhax (Verongida) CO1 has an ORF for a putative LAGLIDADG-type and resembles other sponge and cnidarian mitochondrial introns. Our analysis of the Aplysinella rhax intron underlines that the patchy distribution of introns in sponges is caused by a combination of horizontal and vertical transmission. Further implications for CO1 phylogenetic and barcoding projects are discussed.
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Maikova O, Khanaev I, Belikov S, Sherbakov D. Two hypotheses of the evolution of endemic sponges in Lake Baikal (Lubomirskiidae). J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olga Maikova
- Limnological Institute; Siberian Branch; Russian Academy of Sciences; Irkutsk Russia
| | - Igor Khanaev
- Limnological Institute; Siberian Branch; Russian Academy of Sciences; Irkutsk Russia
| | - Sergei Belikov
- Limnological Institute; Siberian Branch; Russian Academy of Sciences; Irkutsk Russia
| | - Dmitry Sherbakov
- Limnological Institute; Siberian Branch; Russian Academy of Sciences; Irkutsk Russia
- Biological Faculty of Irkutsk State University; Irkutsk Russia
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Breton S, Milani L, Ghiselli F, Guerra D, Stewart DT, Passamonti M. A resourceful genome: updating the functional repertoire and evolutionary role of animal mitochondrial DNAs. Trends Genet 2014; 30:555-64. [PMID: 25263762 DOI: 10.1016/j.tig.2014.09.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 11/24/2022]
Abstract
Recent data from mitochondrial genomics and proteomics research demonstrate the existence of several atypical mitochondrial protein-coding genes (other than the standard set of 13) and the involvement of mtDNA-encoded proteins in functions other than energy production in several animal species including humans. These results are of considerable importance for evolutionary and cellular biology because they indicate that animal mtDNAs have a larger functional repertoire than previously believed. This review summarizes recent studies on animal species with a non-standard mitochondrial functional repertoire and discusses how these genetic novelties represent promising candidates for studying the role of the mitochondrial genome in speciation.
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Affiliation(s)
- Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, 90 Avenue Vincent d'Indy, Montréal, Québec H2V 2S9, Canada.
| | - Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Fabrizio Ghiselli
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Davide Guerra
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donald T Stewart
- Department of Biology, Acadia University, 24 University Avenue, Wolfville, Nova Scotia B4P 2R6, Canada
| | - Marco Passamonti
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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Maier UG, Zauner S, Woehle C, Bolte K, Hempel F, Allen JF, Martin WF. Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes. Genome Biol Evol 2014; 5:2318-29. [PMID: 24259312 PMCID: PMC3879969 DOI: 10.1093/gbe/evt181] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force.
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Affiliation(s)
- Uwe-G Maier
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps-Universität, Marburg, Germany
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del Cerro C, Peñalver A, Cuevas C, de la Calle F, Galán B, García JL. Complete mitochondrial genome of Polymastia littoralis (Demospongiae, Polymastiidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:312-3. [PMID: 24617477 DOI: 10.3109/19401736.2014.892092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Polymastia littoralis (Demospongiae, Polymastiidae) is reported here for the first time. The P. littoralis mitogenome is 21,719 bp base pairs in total length and includes 14 protein-coding gene sequences, small and large rRNA sequences, and 25 tRNA sequences. All genes are encoded on the heavy strand. There are two overlapping genes trnE and nad6.
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Affiliation(s)
- Carlos del Cerro
- a Department of Environmental Biology , Centro de Investigaciones Biológicas (CSIC) , Madrid , Spain and
| | - Ana Peñalver
- b PharmaMar, S.A. Unipersonal , Colmenar , Madrid , Spain
| | - Carmen Cuevas
- b PharmaMar, S.A. Unipersonal , Colmenar , Madrid , Spain
| | | | - Beatriz Galán
- a Department of Environmental Biology , Centro de Investigaciones Biológicas (CSIC) , Madrid , Spain and
| | - José L García
- a Department of Environmental Biology , Centro de Investigaciones Biológicas (CSIC) , Madrid , Spain and
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Yue J, Sun G, Hu X, Huang J. The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis. BMC Genomics 2013; 14:729. [PMID: 24156600 PMCID: PMC4046809 DOI: 10.1186/1471-2164-14-729] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 10/17/2013] [Indexed: 12/29/2022] Open
Abstract
Background It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. Results Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids. Conclusions Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-729) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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Wang Y, Huang XL, Qiao GX. Comparative analysis of mitochondrial genomes of five aphid species (Hemiptera: Aphididae) and phylogenetic implications. PLoS One 2013; 8:e77511. [PMID: 24147014 PMCID: PMC3798312 DOI: 10.1371/journal.pone.0077511] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 09/11/2013] [Indexed: 11/19/2022] Open
Abstract
Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics and population genetics. Only two mitogenomes have been previously released in the insect group Aphididae, which consists of about 5,000 known species including some agricultural, forestry and horticultural pests. Here we report the complete 16,317 bp mitogenome of Cavariella salicicola and two nearly complete mitogenomes of Aphis glycines and Pterocomma pilosum. We also present a first comparative analysis of mitochondrial genomes of aphids. Results showed that aphid mitogenomes share conserved genomic organization, nucleotide and amino acid composition, and codon usage features. All 37 genes usually present in animal mitogenomes were sequenced and annotated. The analysis of gene evolutionary rate revealed the lowest and highest rates for COI and ATP8, respectively. A unique repeat region exclusively in aphid mitogenomes, which included variable numbers of tandem repeats in a lineage-specific manner, was highlighted for the first time. This region may have a function as another origin of replication. Phylogenetic reconstructions based on protein-coding genes and the stem-loop structures of control regions confirmed a sister relationship between Cavariella and pterocommatines. Current evidence suggest that pterocommatines could be formally transferred into Macrosiphini. Our paper also offers methodological instructions for obtaining other Aphididae mitochondrial genomes.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, People's Republic of China
| | - Xiao-Lei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, People's Republic of China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, People's Republic of China
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Redmond NE, Morrow CC, Thacker RW, Diaz MC, Boury-Esnault N, Cardenas P, Hajdu E, Lobo-Hajdu G, Picton BE, Pomponi SA, Kayal E, Collins AG. Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences. Integr Comp Biol 2013; 53:388-415. [DOI: 10.1093/icb/ict078] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol 2013; 13:5. [PMID: 23302374 PMCID: PMC3598815 DOI: 10.1186/1471-2148-13-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 12/21/2012] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. RESULTS We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. CONCLUSIONS Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria.
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Affiliation(s)
- Ehsan Kayal
- Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 20013-7012, Washington, DC, USA
| | - Béatrice Roure
- Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada
| | - Hervé Philippe
- Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada
| | - Allen G Collins
- National Systematics Laboratory of NOAA’s Fisheries Service, National Museum of Natural History, MRC-153, Smithsonian Institution, PO Box 37012, 20013-7012, Washington, DC, USA
| | - Dennis V Lavrov
- Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA
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Zou H, Zhang J, Li W, Wu S, Wang G. Mitochondrial genome of the freshwater jellyfish Craspedacusta sowerbyi and phylogenetics of Medusozoa. PLoS One 2012; 7:e51465. [PMID: 23240028 PMCID: PMC3519871 DOI: 10.1371/journal.pone.0051465] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 11/05/2012] [Indexed: 12/24/2022] Open
Abstract
The 17,922 base pairs (bp) nucleotide sequence of the linear mitochondrial DNA (mtDNA) molecule of the freshwater jellyfish Craspedacusta sowerbyi (Hydrozoa, Trachylina, Limnomedusae) has been determined. This sequence exhibits surprisingly low A+T content (57.1%), containing genes for 13 energy pathway proteins, a small and a large subunit rRNAs, and methionine and tryptophan tRNAs. Mitochondrial ancestral medusozoan gene order (AMGO) was found in the C. sowerbyi, as those found in Cubaia aphrodite (Hydrozoa, Trachylina, Limnomedusae), discomedusan Scyphozoa and Staurozoa. The genes of C. sowerbyi mtDNA are arranged in two clusters with opposite transcriptional polarities, whereby transcription proceeds toward the ends of the DNA molecule. Identical inverted terminal repeats (ITRs) flank the ends of the mitochondrial DNA molecule, a characteristic typical of medusozoans. In addition, two open reading frames (ORFs) of 354 and 1611 bp in length were found downstream of the large subunit rRNA gene, similar to the two ORFs of ORF314 and polB discovered in the linear mtDNA of C. aphrodite, discomedusan Scyphozoa and Staurozoa. Phylogenetic analyses of C. sowerbyi and other cnidarians were carried out based on both nucleotide and inferred amino acid sequences of the 13 mitochondrial energy pathway genes. Our working hypothesis supports the monophyletic Medusozoa being a sister group to Octocorallia (Cnidaria, Anthozoa). Within Medusozoa, the phylogenetic analysis suggests that Staurozoa may be the earliest diverging class and the sister group of all other medusozoans. Cubozoa and coronate Scyphozoa form a clade that is the sister group of Hydrozoa plus discomedusan Scyphozoa. Hydrozoa is the sister group of discomedusan Scyphozoa. Semaeostomeae is a paraphyletic clade with Rhizostomeae, while Limnomedusae (Trachylina) is the sister group of hydroidolinans and may be the earliest diverging lineage among Hydrozoa.
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Affiliation(s)
- Hong Zou
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Graduate School of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Jin Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Graduate School of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Wenxiang Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
| | - Shangong Wu
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
| | - Guitang Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, P.R. China
- * E-mail:
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Imešek M, Pleše B, Lukić-Bilela L, Lelo S, Ćetković H. Mitochondrial genomes of the genus Ephydatia Lamouroux, 1816: can palindromic elements be used in species-level studies? ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0118-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lavrov DV, Pett W, Voigt O, Wörheide G, Forget L, Lang BF, Kayal E. Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): six linear chromosomes, fragmented rRNAs, tRNA editing, and a novel genetic code. Mol Biol Evol 2012; 30:865-80. [PMID: 23223758 DOI: 10.1093/molbev/mss274] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sponges (phylum Porifera) are a large and ancient group of morphologically simple but ecologically important aquatic animals. Although their body plan and lifestyle are relatively uniform, sponges show extensive molecular and genetic diversity. In particular, mitochondrial genomes from three of the four previously studied classes of Porifera (Demospongiae, Hexactinellida, and Homoscleromorpha) have distinct gene contents, genome organizations, and evolutionary rates. Here, we report the mitochondrial genome of Clathrina clathrus (Calcinea, Clathrinidae), a representative of the fourth poriferan class, the Calcarea, which proves to be the most unusual. Clathrina clathrus mitochondrial DNA (mtDNA) consists of six linear chromosomes 7.6-9.4 kb in size and encodes at least 37 genes: 13 protein codings, 2 ribosomal RNAs (rRNAs), and 24 transfer RNAs (tRNAs). Protein genes include atp9, which has now been found in all major sponge lineages, but no atp8. Our analyses further reveal the presence of a novel genetic code that involves unique reassignments of the UAG codons from termination to tyrosine and of the CGN codons from arginine to glycine. Clathrina clathrus mitochondrial rRNAs are encoded in three (srRNA) and ≥6 (lrRNA) fragments distributed out of order and on several chromosomes. The encoded tRNAs contain multiple mismatches in the aminoacyl acceptor stems that are repaired posttranscriptionally by 3'-end RNA editing. Although our analysis does not resolve the phylogenetic position of calcareous sponges, likely due to their high rates of mitochondrial sequence evolution, it confirms mtDNA as a promising marker for population studies in this group. The combination of unusual mitochondrial features in C. clathrus redefines the extremes of mtDNA evolution in animals and further argues against the idea of a "typical animal mtDNA."
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, USA.
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Brockman SA, McFadden CS. The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes. Genome Biol Evol 2012; 4:994-1006. [PMID: 22975720 PMCID: PMC3468961 DOI: 10.1093/gbe/evs074] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.
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Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 2012; 69:313-9. [PMID: 22982435 DOI: 10.1016/j.ympev.2012.08.023] [Citation(s) in RCA: 3417] [Impact Index Per Article: 284.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 07/11/2012] [Accepted: 08/27/2012] [Indexed: 11/16/2022]
Abstract
About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.
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Affiliation(s)
- Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, University Leipzig, Augustusplatz 10-11, 04109 Leipzig, Germany.
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Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges. Gene 2012; 505:91-9. [PMID: 22669046 DOI: 10.1016/j.gene.2012.05.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/31/2022]
Abstract
Demosponges, the largest and most diverse class in the phylum Porifera, possess mitochondrial DNA (mtDNA) markedly different from that in other animals. Although several studies investigated evolution of demosponge mtDNA among major lineages of the group, the changes within these groups remain largely unexplored. Recently we determined mitochondrial genomic sequence of the Lake Baikal sponge Lubomirskia baicalensis and described proliferation of small inverted repeats (hairpins) that occurred in it since the divergence between L. baicalensis and the most closely related cosmopolitan freshwater sponge Ephydatia muelleri. Here we report mitochondrial genomes of three additional species of Lake Baikal sponges: Swartschewskia papyracea, Rezinkovia echinata and Baikalospongia intermedia morpha profundalis (Demospongiae, Haplosclerida, Lubomirskiidae) and from a more distantly related freshwater sponge Corvomeyenia sp. (Demospongiae, Haplosclerida, Metaniidae). We use these additional sequences to explore mtDNA evolution in Baikalian sponges, paying particular attention to the variation in the rates of nucleotide substitutions and the distribution of hairpins, abundant in these genomes. We show that most of the changes in Lubomirskiidae mitochondrial genomes are due to insertion/deletion/duplication of these elements rather than single nucleotide substitutions. Thus inverted repeats can act as an important force in evolution of mitochondrial genome architecture and be a valuable marker for population- and species-level studies in this group. In addition, we infer (((Rezinkovia+Lubomirskia)+Swartschewskia)+Baikalospongia) phylogeny for the family Lubomirskiidae based on the analysis of mitochondrial coding sequences from freshwater sponges.
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Abstract
Knowledge of the functioning, health state, and capacity for recovery of marine benthic organisms and assemblages has become essential to adequately manage and preserve marine biodiversity. Molecular tools have allowed an entirely new way to tackle old and new questions in conservation biology and ecology, and sponge science is following this lead. In this review, we discuss the biological and ecological studies of sponges that have used molecular markers during the past 20 years and present an outlook for expected trends in the molecular ecology of sponges in the near future. We go from (1) the interface between inter- and intraspecies studies, to (2) phylogeography and population level analyses, (3) intra-population features such as clonality and chimerism, and (4) environmentally modulated gene expression. A range of molecular markers has been assayed with contrasting success to reveal cryptic species and to assess the genetic diversity and connectivity of sponge populations, as well as their capacity to respond to environmental changes. We discuss the pros and cons of the molecular gene partitions used to date and the prospects of a plentiful supply of new markers for sponge ecological studies in the near future, in light of recently available molecular technologies. We predict that molecular ecology studies of sponges will move from genetics (the use of one or some genes) to genomics (extensive genome or transcriptome sequencing) in the forthcoming years and that sponge ecologists will take advantage of this research trend to answer ecological and biological questions that would have been impossible to address a few years ago.
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Affiliation(s)
- Maria J Uriz
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Girona, Spain.
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Wörheide G, Dohrmann M, Erpenbeck D, Larroux C, Maldonado M, Voigt O, Borchiellini C, Lavrov DV. Deep phylogeny and evolution of sponges (phylum Porifera). ADVANCES IN MARINE BIOLOGY 2012; 61:1-78. [PMID: 22560777 DOI: 10.1016/b978-0-12-387787-1.00007-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a comprehensive understanding of the relationships among and within the main sponge lineages to fully appreciate the evolution of this extraordinary metazoan phylum.
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Affiliation(s)
- G Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany.
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Suzuki T, Miyauchi K, Suzuki T, Yokobori SI, Shigi N, Kondow A, Takeuchi N, Yamagishi A, Watanabe K. Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria. J Biol Chem 2011; 286:35494-35498. [PMID: 21873425 PMCID: PMC3195572 DOI: 10.1074/jbc.m111.279810] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/09/2011] [Indexed: 11/06/2022] Open
Abstract
Variations in the genetic code are found frequently in mitochondrial decoding systems. Four non-universal genetic codes are employed in ascidian mitochondria: AUA for Met, UGA for Trp, and AGA/AGG(AGR) for Gly. To clarify the decoding mechanism for the non-universal genetic codes, we isolated and analyzed mitochondrial tRNAs for Trp, Met, and Gly from an ascidian, Halocynthia roretzi. Mass spectrometric analysis identified 5-taurinomethyluridine (τm(5)U) at the anticodon wobble positions of tRNA(Met)(AUR), tRNA(Trp)(UGR), and tRNA(Gly)(AGR), suggesting that τm(5)U plays a critical role in the accurate deciphering of all four non-universal codes by preventing the misreading of pyrimidine-ending near-cognate codons (NNY) in their respective family boxes. Acquisition of the wobble modification appears to be a prerequisite for the genetic code alteration.
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Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shin-Ichi Yokobori
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Naoki Shigi
- Biomedicinal Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Akiko Kondow
- Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Nono Takeuchi
- Department of Medical Genome, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwa, Chiba 277-8652, Japan
| | - Akihiko Yamagishi
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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Watanabe K, Yokobori SI. tRNA Modification and Genetic Code Variations in Animal Mitochondria. J Nucleic Acids 2011; 2011:623095. [PMID: 22007289 PMCID: PMC3191813 DOI: 10.4061/2011/623095] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/04/2011] [Indexed: 12/03/2022] Open
Abstract
In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons (tRNATrp for UGA, tRNAMet for AUA, tRNAAsn for AAA, and tRNASer and tRNAGly for AGA/AGG) are all modified; tRNATrp has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, tRNAMet has 5-formylcytidine or 5-taurinomethyluridine, tRNASer has 7-methylguanosine and tRNAGly has 5-taurinomethyluridine in their anticodon wobble position, and tRNAAsn has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.
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Affiliation(s)
- Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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Park E, Song JI, Won YJ. The complete mitochondrial genome of Calicogorgia granulosa (Anthozoa: Octocorallia): potential gene novelty in unidentified ORFs formed by repeat expansion and segmental duplication. Gene 2011; 486:81-7. [PMID: 21798322 DOI: 10.1016/j.gene.2011.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 06/29/2011] [Accepted: 07/07/2011] [Indexed: 01/24/2023]
Abstract
Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,246 bp of the complete mitogenome, which is the largest among the nine octocorals sequenced to date, contains 13 protein coding genes, 2 rRNAs and a tRNA within its circular form of mitochondrial DNA. We found an identical segmental duplication (S1 and S2, 913 bp) composed of an ORF (672 bp) coding for a hypothetical protein within which Direct Variant Repeat (DVR) expansions reside in-frame to the coding sequence. Additionally, the duplicated segmental DNA showed no variation in nucleotide sequences both between S1 and S2 and across multiple individual samples. Upon these observations, we discuss plausible causes for the intramitochondrial segmental duplication and the absence of sequence variation, and a need for further investigation of the novel ORF as well. In conclusion the present mitogenome of C. granulosa adds more information to our understanding of the diversity and evolution of mitogenomes of nonbilaterian animals.
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Affiliation(s)
- Eunji Park
- Division of EcoScience, Ewha Womans University, Sodaemun-Gu, Seoul, Republic of Korea
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Maikova OO, Itskovich VB, Semiturkina NA, Kaluzhnaya OV, Belikov SI. Phylogenetic position of sponges from Chagatai and Tore-Khol lakes. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410120100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gazave E, Lapébie P, Renard E, Vacelet J, Rocher C, Ereskovsky AV, Lavrov DV, Borchiellini C. Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (Porifera, Homoscleromorpha). PLoS One 2010; 5:e14290. [PMID: 21179486 PMCID: PMC3001884 DOI: 10.1371/journal.pone.0014290] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 11/16/2010] [Indexed: 01/02/2023] Open
Abstract
Background Homoscleromorpha is the fourth major sponge lineage, recently recognized to be distinct from the Demospongiae. It contains <100 described species of exclusively marine sponges that have been traditionally subdivided into 7 genera based on morphological characters. Because some of the morphological features of the homoscleromorphs are shared with eumetazoans and are absent in other sponges, the phylogenetic position of the group has been investigated in several recent studies. However, the phylogenetic relationships within the group remain unexplored by modern methods. Methodology/Principal Findings Here we describe the first molecular phylogeny of Homoscleromorpha based on nuclear (18S and 28S rDNA) and complete mitochondrial DNA sequence data that focuses on inter-generic relationships. Our results revealed two robust clades within this group, one containing the spiculate species (genera Plakina, Plakortis, Plakinastrella and Corticium) and the other containing aspiculate species (genera Oscarella and Pseudocorticium), thus rejecting a close relationship between Pseudocorticium and Corticium. Among the spiculate species, we found affinities between the Plakortis and Plakinastrella genera, and between the Plakina and Corticium. The validity of these clades is furthermore supported by specific morphological characters, notably the type of spicules. Furthermore, the monophyly of the Corticium genus is supported while the monophyly of Plakina is not. Conclusions/Significance As the result of our study we propose to restore the pre-1995 subdivision of Homoscleromorpha into two families: Plakinidae Schulze, 1880 for spiculate species and Oscarellidae Lendenfeld, 1887 for aspiculate species that had been rejected after the description of the genus Pseudocorticium. We also note that the two families of homoscleromorphs exhibit evolutionary stable, but have drastically distinct mitochondrial genome organizations that differ in gene content and gene order.
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Affiliation(s)
- Eve Gazave
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Pascal Lapébie
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Emmanuelle Renard
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Jean Vacelet
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Caroline Rocher
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
| | - Alexander V. Ereskovsky
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
- Department of Embryology, Faculty of Biology and Soils, Saint-Petersburg State University, St Petersburg, Russia
| | - Dennis V. Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Iowa, Ames, United States of America
| | - Carole Borchiellini
- Aix-Marseille Université, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, Marseilles, France
- * E-mail:
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Szitenberg A, Rot C, Ilan M, Huchon D. Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae. BMC Evol Biol 2010; 10:288. [PMID: 20849667 PMCID: PMC2955029 DOI: 10.1186/1471-2148-10-288] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/20/2010] [Indexed: 01/31/2023] Open
Abstract
Background Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family. Results Seventeen tetillid cox 1 sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the cox 1 alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives) and their nesting cox 1 sequences. Reciprocal AU tests indicated that the intron and cox 1 tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant. Conclusions The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely explain the current distribution of metazoan group I introns. An alternative scenario that includes horizontal gene transfer events appears to be more suitable to explain the incongruence between the intron 723 and the cox 1 topologies. In addition, our results suggest that three different intron forms independently colonized the cox 1 gene of tetillids. Among sponges, the Tetillidae family seems to be experiencing an unusual number of intron insertions.
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Affiliation(s)
- Amir Szitenberg
- Department of Zoology, Tel-Aviv University, Tel Aviv 69978, Israel
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Daly M, Gusmao LC, Reft AJ, Rodriguez E. Phylogenetic Signal in Mitochondrial and Nuclear Markers in Sea Anemones (Cnidaria, Actiniaria). Integr Comp Biol 2010; 50:371-88. [DOI: 10.1093/icb/icq081] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schierwater B, Kamm K. The Early Evolution of Hox Genes: A Battle of Belief? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:81-90. [DOI: 10.1007/978-1-4419-6673-5_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Cárdenas P, Rapp HT, Schander C, Tendal OS. Molecular taxonomy and phylogeny of the Geodiidae (Porifera,Demospongiae, Astrophorida) â combining phylogenetic and Linnaean classification. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00402.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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50
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Erpenbeck D, Voigt O, Wörheide G, Lavrov DV. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE). BMC Genomics 2009; 10:591. [PMID: 20003196 PMCID: PMC2800124 DOI: 10.1186/1471-2164-10-591] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 12/09/2009] [Indexed: 01/14/2023] Open
Abstract
Background The mitochondrial (mt) genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida) and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.
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Affiliation(s)
- Dirk Erpenbeck
- Department of Earth- and Environmental Sciences, Palaeontology & Geobiology and GeoBioCenter LMU, Ludwig-Maximilians Universität München, Richard-Wagner-Str, 10, 80333 München, Germany.
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